def setUp(self):
super().setUp()
self.project = ProjectFactory()
variant_sets = SmallVariantSetFactory.create_batch(
2, case__project=self.project)
SmallVariantFactory(variant_set=variant_sets[0])
SmallVariantFactory(variant_set=variant_sets[1])
for variant_set in variant_sets:
update_variant_counts(variant_set.case)
def setUp(self):
super().setUp()
user = self.make_user("superuser")
self.bgjob = ProjectCasesFilterBgJobFactory(user=user)
variant_sets = SmallVariantSetFactory.create_batch(
2, case__project=self.bgjob.project)
SmallVariantFactory.create_batch(3, variant_set=variant_sets[0])
SmallVariantFactory.create_batch(3, variant_set=variant_sets[1])
self.bgjob.projectcasessmallvariantquery.query_settings.update(
vars(FormDataFactory(names=self.bgjob.project.get_members())))
def setUp(self):
self.user = self.make_user("superuser")
self.variant_set_active_above_thres = SmallVariantSetFactory(state="active")
self.variant_set_active_above_thres.date_created = datetime.now() - timedelta(hours=1)
self.variant_set_active_above_thres.save()
self.variant_set_inactive_above_thres = SmallVariantSetFactory(state="importing")
self.variant_set_inactive_above_thres.date_created = datetime.now() - timedelta(hours=2)
self.variant_set_inactive_above_thres.save()
self.variant_set_active_below_thres = SmallVariantSetFactory(state="active")
self.variant_set_active_below_thres.date_created = datetime.now() - timedelta(hours=13)
self.variant_set_active_below_thres.save()
self.variant_set_inactive_below_thres = SmallVariantSetFactory(state="importing")
self.variant_set_inactive_below_thres.date_created = datetime.now() - timedelta(hours=14)
self.variant_set_inactive_below_thres.save()
def setUp(self):
self.user = self.make_user("superuser")
variant_set = SmallVariantSetFactory()
self.bg_job = BackgroundJob.objects.create(
name="job name",
project=Project.objects.first(),
job_type="variants.export_file_bg_job",
user=self.user,
)
self.export_job = ExportFileBgJob.objects.create(
project=self.bg_job.project,
bg_job=self.bg_job,
case=variant_set.case,
query_args={"some": "args"},
file_type="xlsx",
)
def setUp(self):
super().setUp()
self.variant_set = SmallVariantSetFactory()
self.hponame = HpoNameFactory(hpo_id="HP:0000001")
self.hpos = [
HpoFactory(
database_id="OMIM:000001",
hpo_id="HP:0000002",
name="Disease 1;;Alternative Description",
),
HpoFactory(
database_id="OMIM:000001",
hpo_id="HP:0000003",
name="Disease 1;;Alternative Description",
),
]
self.maxDiff = None
def setUp(self):
self.user = self.make_user("superuser")
self.variant_set = SmallVariantSetFactory()
self.small_vars = SmallVariantFactory.create_batch(3, variant_set=self.variant_set)
self.case = self.variant_set.case
self.bg_job = BackgroundJob.objects.create(
name="job name",
project=Project.objects.first(),
job_type="variants.export_file_bg_job",
user=self.user,
)
self.export_job = ExportFileBgJob.objects.create(
project=self.bg_job.project,
bg_job=self.bg_job,
case=self.case,
query_args={"export_flags": True, "export_comments": True},
file_type="xlsx",
)
def setUp(self):
super().setUp()
self.variant_set = SmallVariantSetFactory()
self.hpo_id = "HP:0000001"
self.case = self.variant_set.case
self.user = self.make_user("superuser")
self.small_vars = [
SmallVariantFactory(chromosome="1",
refseq_gene_id="1234",
variant_set=self.variant_set),
SmallVariantFactory(chromosome="1",
refseq_gene_id="2234",
variant_set=self.variant_set),
SmallVariantFactory(chromosome="1",
refseq_gene_id="2234",
variant_set=self.variant_set,
in_clinvar=True),
]
self.bgjob = FilterBgJobFactory(case=self.case, user=self.user)
class TestCleanupVariantSets(TestCase):
def setUp(self):
self.user = self.make_user("superuser")
self.variant_set_active_above_thres = SmallVariantSetFactory(state="active")
self.variant_set_active_above_thres.date_created = datetime.now() - timedelta(hours=1)
self.variant_set_active_above_thres.save()
self.variant_set_inactive_above_thres = SmallVariantSetFactory(state="importing")
self.variant_set_inactive_above_thres.date_created = datetime.now() - timedelta(hours=2)
self.variant_set_inactive_above_thres.save()
self.variant_set_active_below_thres = SmallVariantSetFactory(state="active")
self.variant_set_active_below_thres.date_created = datetime.now() - timedelta(hours=13)
self.variant_set_active_below_thres.save()
self.variant_set_inactive_below_thres = SmallVariantSetFactory(state="importing")
self.variant_set_inactive_below_thres.date_created = datetime.now() - timedelta(hours=14)
self.variant_set_inactive_below_thres.save()
def test_cleanup_variant_sets(self):
self.assertEqual(SmallVariantSet.objects.all().count(), 4)
cleanup_variant_sets()
variant_sets = SmallVariantSet.objects.all().order_by("-date_created")
self.assertEqual(variant_sets.count(), 3)
self.assertEqual(variant_sets[0].id, self.variant_set_active_above_thres.id)
self.assertEqual(variant_sets[1].id, self.variant_set_inactive_above_thres.id)
self.assertEqual(variant_sets[2].id, self.variant_set_active_below_thres.id)
def setUp(self):
super().setUp()
variant_set = SmallVariantSetFactory()
self.case = variant_set.case
small_var = SmallVariantFactory(variant_set=variant_set)
def setUp(self):
super().setUp()
variant_set = SmallVariantSetFactory()
self.case = variant_set.case
SampleVariantStatisticsFactory(variant_set=variant_set,
sample_name=variant_set.case.index)